Examples with BlatAssociation ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation used on opensource projects

Example 21 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class BlatAssociationDaoImpl method thaw.

@Override
public void thaw(final Collection<BlatAssociation> blatAssociations) {
    if (blatAssociations == null)
        return;
    HibernateTemplate templ = this.getHibernateTemplate();
    templ.executeWithNativeSession(new org.springframework.orm.hibernate3.HibernateCallback<Object>() {

        @Override
        public Object doInHibernate(org.hibernate.Session session) throws org.hibernate.HibernateException {
            for (Object object : blatAssociations) {
                BlatAssociation blatAssociation = (BlatAssociation) object;
                if ((blatAssociation).getId() == null)
                    continue;
                BlatAssociationDaoImpl.this.thawBlatAssociation(session, blatAssociation);
                session.evict(blatAssociation);
            }
            return null;
        }
    });
}

Example 22 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class BlatAssociationScorerTest method testScoreResults.

@Test
public void testScoreResults() {
    // there's only one gene product that is aligned to two different regions
    GeneProduct geneProduct = this.createGeneProduct();
    BlatResult blatResult_1 = this.createBlatResult("6_cox_hap2");
    BlatResult blatResult_2 = this.createBlatResult("6");
    // this has the highest score but located on a non-canonical chromosome
    // so this should be ignored
    BlatAssociation association_1 = BlatAssociation.Factory.newInstance();
    association_1.setGeneProduct(geneProduct);
    association_1.setBlatResult(blatResult_1);
    association_1.setScore(50.0);
    association_1.setOverlap(50);
    association_1.setBioSequence(BioSequence.Factory.newInstance());
    BlatAssociation association_2 = BlatAssociation.Factory.newInstance();
    association_2.setGeneProduct(geneProduct);
    association_2.setBlatResult(blatResult_2);
    association_2.setScore(30.0);
    association_2.setOverlap(30);
    association_2.setBioSequence(BioSequence.Factory.newInstance());
    Collection<BlatAssociation> blatAssociations = new ArrayList<>();
    blatAssociations.add(association_1);
    blatAssociations.add(association_2);
    ProbeMapperConfig config = new ProbeMapperConfig();
    config.setTrimNonCanonicalChromosomeHits(true);
    // BlatAssociation expected = association_2;
    BlatAssociation actual = BlatAssociationScorer.scoreResults(blatAssociations);
    assertFalse(ChromosomeUtil.isCanonical(blatResult_1.getTargetChromosome()));
    assertTrue(ChromosomeUtil.isCanonical(blatResult_2.getTargetChromosome()));
    assertEquals(940.0, association_1.getScore(), 0);
    assertEquals(564.0, association_2.getScore(), 0);
    assertEquals(1.0, actual.getSpecificity(), 0);
// assertEquals( expected, actual );
}

Example 23 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class GoldenPathSequenceAnalysis method computeLocationInGene.

/**
 * Given a location and a gene product, compute the distance from the 3' end of the gene product as well as the
 * amount of overlap. If the location has low overlaps with known exons (threshold set by
 * RECHECK_OVERLAP_THRESHOLD), we optionally search for mRNAs in the region. If there are overlapping mRNAs, we use
 * the best overlap value. If the overlap is still not high enough we optionally check ESTs.
 *
 * @param chromosome chromosome
 * @param queryStart start
 * @param queryEnd end
 * @param starts Start locations of alignments of the query (target coordinates)
 * @param sizes Sizes of alignments of the query.
 * @param geneProduct GeneProduct with which the overlap and distance is to be computed.
 * @param method method
 * @param config The useEsts and useRNA options are relevant
 * @return a ThreePrimeData object containing the results.
 */
private BlatAssociation computeLocationInGene(String chromosome, Long queryStart, Long queryEnd, String starts, String sizes, GeneProduct geneProduct, ThreePrimeDistanceMethod method, ProbeMapperConfig config) {
    assert geneProduct != null : "GeneProduct is null";
    BlatAssociation blatAssociation = BlatAssociation.Factory.newInstance();
    blatAssociation.setGeneProduct(geneProduct);
    blatAssociation.setThreePrimeDistanceMeasurementMethod(method);
    PhysicalLocation geneLoc = geneProduct.getPhysicalLocation();
    assert geneLoc != null : "PhysicalLocation for GeneProduct " + geneProduct + " is null";
    assert geneLoc.getNucleotide() != null;
    int geneStart = geneLoc.getNucleotide().intValue();
    int geneEnd = geneLoc.getNucleotide().intValue() + geneLoc.getNucleotideLength();
    int exonOverlap = 0;
    if (starts != null & sizes != null) {
        exonOverlap = SequenceManipulation.getGeneProductExonOverlap(starts, sizes, geneLoc.getStrand(), geneProduct);
        int totalSize = SequenceManipulation.totalSize(sizes);
        if (config.isUseMrnas() && exonOverlap / (double) (totalSize) < GoldenPathSequenceAnalysis.RECHECK_OVERLAP_THRESHOLD) {
            int newOverlap = this.checkRNAs(chromosome, queryStart, queryEnd, starts, sizes, exonOverlap, geneLoc.getStrand(), geneProduct.getGene());
            if (newOverlap > exonOverlap) {
                GoldenPath.log.debug("mRNA overlap was higher than primary transcript");
                exonOverlap = newOverlap;
            }
        }
        if (config.isUseEsts() && exonOverlap / (double) (totalSize) < GoldenPathSequenceAnalysis.RECHECK_OVERLAP_THRESHOLD) {
            int newOverlap = this.checkESTs(chromosome, queryStart, queryEnd, starts, sizes, exonOverlap, geneLoc.getStrand());
            if (newOverlap > exonOverlap) {
                GoldenPath.log.debug("Exon overlap was higher than mrna or  primary transcript");
                exonOverlap = newOverlap;
            }
        }
        assert exonOverlap <= totalSize;
    }
    blatAssociation.setOverlap(exonOverlap);
    if (method == ThreePrimeDistanceMethod.MIDDLE) {
        int center = SequenceManipulation.findCenter(starts, sizes);
        if (geneLoc.getStrand().equals("+")) {
            // then the 3' end is at the 'end'. : >>>>>>>>>>>>>>>>>>>>>*>>>>> (* is where we might be)
            blatAssociation.setThreePrimeDistance((long) Math.max(0, geneEnd - center));
        } else if (geneProduct.getPhysicalLocation().getStrand().equals("-")) {
            // then the 3' end is at the 'start'. : <<<*<<<<<<<<<<<<<<<<<<<<<<<
            blatAssociation.setThreePrimeDistance((long) Math.max(0, center - geneStart));
        } else {
            throw new IllegalArgumentException("Strand wasn't '+' or '-'");
        }
    } else if (method == ThreePrimeDistanceMethod.RIGHT) {
        if (geneLoc.getStrand().equals("+")) {
            // then the 3' end is at the 'end'. : >>>>>>>>>>>>>>>>>>>>>*>>>>> (* is where we might be)
            blatAssociation.setThreePrimeDistance(Math.max(0, geneEnd - queryEnd));
        } else if (geneProduct.getPhysicalLocation().getStrand().equals("-")) {
            // then the 3' end is at the 'start'. : <<<*<<<<<<<<<<<<<<<<<<<<<<<
            blatAssociation.setThreePrimeDistance(Math.max(0, queryStart - geneStart));
        } else {
            throw new IllegalArgumentException("Strand wasn't '+' or '-'");
        }
    } else if (method == ThreePrimeDistanceMethod.LEFT) {
        throw new UnsupportedOperationException("Left edge measure not supported");
    } else {
        throw new IllegalArgumentException("Unknown method");
    }
    return blatAssociation;
}

Example 24 with BlatAssociation

use of ubic.gemma.model.genome.sequenceAnalysis.BlatAssociation in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestPersistentBioSequence2GeneProducts.

/**
 * @param bioSequence bio sequence
 * @return bio sequence to gene products
 */
public Collection<BioSequence2GeneProduct> getTestPersistentBioSequence2GeneProducts(BioSequence bioSequence) {
    Collection<BioSequence2GeneProduct> b2gCol = new HashSet<>();
    BlatAssociation b2g = BlatAssociation.Factory.newInstance();
    b2g.setScore(new Random().nextDouble());
    b2g.setBioSequence(bioSequence);
    b2g.setGeneProduct(this.getTestPersistentGeneProduct(this.getTestPersistentGene()));
    b2g.setBlatResult(this.getTestPersistentBlatResult(bioSequence, null));
    b2gCol.add(b2g);
    // noinspection unchecked
    return (Collection<BioSequence2GeneProduct>) persisterHelper.persist(b2gCol);
}